tbuckley/cabot-search huggingface dataset:
HGG-21. ABERRANT SPLICING OF CLK1 IN PEDIATRIC HIGH-GRADE GLIOMAS DISRUPTS KEY ONCOGENIC TRANSCRIPTIONAL PROGRAMS
Authors: Ammar Naqvi, Brian Ennis, Ryan Corbett, Aditya Lahiri, Zhuangzhuang Geng, Run Kin, Krutika Gaonkar, Komal Rathi, Karina Conkrite, Priyanka Seghal, Katharina Hayer, Adam Kraya, Jessica Foster, Peter Madsen, Andrei Thomas-Tikhonenko, Phillip Storm, Adam Resnick, Jo Lynne Rokita
Journal: Neuro-Oncology (2023)

Abstract While the majority of somatic DNA coding alterations in pediatric brain tumors have been profiled, studies exploring transcriptional mechanisms remain underexplored. We systematically characterized aberrant splicing in primary tumors of seven broad histologies of pediatric brain tumors. We obtained RNA-seq data (n = 792) from the Open Pediatric Brain Tumor Atlas and integrated rMATs splice event calls with UniProt Knowledgebase to quantify and prioritize differential alternative splicing events with proteomic potential. We identified three splicing-driven biological clusters and found pediatric high-grade gliomas (pHGGs) to be uniquely heterogeneous, spanning all three clusters. We also discovered that tumors with high splicing burden (SB) had significantly worse overall survival than tumors with low SB (p &amp;lt; 1x10-4). Furthermore, pHGGs (n = 154) displayed the greatest splicing heterogeneity with 20,620 exon splicing aberrations (pval/FDR &amp;lt; 0.05) in 3,294 genes that resulted in a gain or loss of known functional sites. We prioritized targetable kinases and found that CDC-like kinase 1 (CLK1), a known modulator of master splicing regulators, exhibited significantly increased exon 4 inclusion (p &amp;lt; 0.05, ΔPSI &amp;gt;= |.20|), and subsequent gain of two phosphorylation sites, in tumors compared to matched non-tumor tissue. Exon 4 inclusion was significantly correlated with increased CLK1 expression (r = 0.57, p = 7.8 x10-9), which we posit results in hyper-activity of CLK1 and aberrant splicing of its targets in these tumors. Furthermore, predicted CLK1 gene targets (n = 101) were enriched for cancer-related pathways, such as DNA repair (odds ratio &amp;gt; 2, p &amp;lt; 0.005). In summary, we describe aberrant splicing in pHGGs as an alternative mechanism that could drive tumorigenesis. Future work will focus on molecular validation and therapeutic targeting of CLK1 in available pHGG models, potentially opening new therapeutic strategies in children with brain tumors.
Troubleshooting for difficult removal of a stent delivery system after endoscopic ultrasound-guided hepaticogastrostomy
Authors: Takeshi Ogura, Taro Iwatsubo, Jun Sakamoto, Junichi Nakamura, Masahiro Yamamura, Hiroki Nishikawa
Journal: Endoscopy (2023)

Endoscopic ultrasound-guided hepaticogastrostomy (EUS-HGS) is now widely performed for patients in whom endoscopic retrograde cholangiopancreatography is unsuccessful [1] [2] [3] [4]. Various technical tips have been reported for preventing adverse events and improving the technical success rate before stent deployment. We herein describe a troubleshooting technique for difficult removal of the stent delivery system after EUS-HGS stent deployment.
IMMU-10. PILOCYTIC ASTROCYTOMAS SHOW EVIDENCE OF INTRINSIC IMMUNE SURVEILLANCE AND ACTIVATION WITHIN THE TUMOR MICROENVIRONMENT
Authors: Hinda Najem, Shashwat Tripathi, Kathleen McCortney, Victoria Jane Horak, Kaethe Leonard, Alicia Steffens, Jordain Walshon, Craig M Horbinski, Nitin R Wadhwani, Charles David James, Sandi Lam, Maciej S Lesniak, Jared K Burks, Amy B Heimberger, Michael G DeCuypere
Journal: Neuro-Oncology (2023)

Abstract PURPOSE To clarify the immunoreactivity and potential immunotherapeutic targets of pediatric low- and high-grade gliomas (HGG). METHODS Spatial sequential immunofluorescence (seqIFTM) of 24 protein markers, NanoString analysis of 770 immune genes, and scRNA sequencing were used to profile and characterize the tumor microenvironment (TME) of 13 newly diagnosed WHO grade 1 pilocytic astrocytomas (PA), 6 pediatric HGG, and 3 normal brain (NB) samples. RESULTS Relative to NB, HGGs were enriched with T cells, cancer-associated fibroblasts (CAF), CD11c+ antigen-presenting cells, and CD163+ macrophages. In contrast, PA showed more CD11c+P2RY12+ microglia and CD11c+CD205+ dendritic cells (DCs). TMEM119+ microglia were present in NB and brain adjacent to PA but were rare within the TME of all gliomas regardless of histology. PA uniquely contained naïve CD45RO-FoxP3-PD-1-TIM-3-LAG-3- T cells forming immunological synapses, as visualized by Lck+ expression at the membrane interfaces, during interaction with either microglia or DCs. This finding was not encountered in HGG. TIM-3 was the most frequently expressed immune modulatory target on all the myeloid populations, regardless of tumor histology. PD-L1 expression, especially on microglia, was more frequent in PA than in HGG. NanoString analysis revealed the pro-inflammatory and enabler of diapedesis IL-1 pathway genes (IL1RAP, TICAM2, and IRAK4) were upregulated in PA relative to the matched adjacent brain using unsupervised hierarchical clustering. CONCLUSIONS Based on multiple orthogonal analysis strategies, PAs display a more pro-inflammatory phenotype, in comparison to HGG, suggesting immunological surveillance that may be driven by IL-1, as a baseline feature at presentation.
XRT-01. LONG-TERM HEARING LOSS IN CHILDREN WITH MEDULLOBLASTOMA AFTER PROTON IRRADIATION AND CHEMOTHERAPY
Authors: Mohammad H Abu-Arja, Austin L Brown, Jack M Su, M Fatih Okcu, Holly B Lindsay, Susan L McGovern, Mary Frances McAleer, David R Grosshans, Murali M Chintagumpala, Arnold C Paulino
Journal: Neuro-Oncology (2023)

Abstract PURPOSE To evaluate the incidence and risk factors for hearing loss (HL) among children with medulloblastoma treated with proton irradiation and cisplatin. METHODS We identified children with medulloblastoma ≥3 years of age treated at Texas Children’s Hospital between 2007-2022. Audiograms were graded using the International Society of Pediatric Oncology-Boston scale (SIOP-Boston). Time to grade ≥3 HL was evaluated using Kaplan-Meier and multivariable Cox models to estimate hazard ratios (HR) and 95% confidence intervals (CI). RESULTS Seventy-eight patients (65.4% male) were treated with craniospinal irradiation (CSI) at a median age of 7.6 years (range: 3-21). The mean cochlear irradiation dose was 31.5±9 Gy, and the cumulative cisplatin dose was 295±50 mg/m2. Fifty-six patients (72%) received amifostine. Patients completed a median of 9 audiograms (range: 4-22) with a median audiogram follow-up of 49 months (range: 3-177). Grade ≥3 HL was documented in 25 patients (32%). In adjusted Cox models, mean cochlear dose (HR=1.12, 95% CI: 1.06-1.18) and the age at CSI (HR=0.81, 95% CI: 0.68-0.98) were associated with grade ≥3 HL. Among children who received irradiation after or at 7 years of age, the estimated probability of grade ≥3 HL at three years post-CSI was 12.6% (95% CI: 4.1-34.6) in children exposed to &amp;lt;36 Gy cochlear irradiation and 35.6% (95% CI: 17.4-63.6) in children exposed to &amp;gt;36 Gy cochlear irradiation. Among children who received irradiation before 7 years of age, the estimated probability of grade ≥3 HL at three years post-CSI was 16.5% (95% CI: 5.6-43) in children exposed to &amp;lt;36 Gy cochlear radiation and 66.7% (95% CI: 35.4-93.7) in children exposed to &amp;gt;36 Gy cochlear irradiation. CONCLUSION Long-term follow-up shows that children who received a cochlear dose ≥36 Gy before 7 years of age are at higher risk for HL, regardless of the amifostine and the cisplatin dose.
Closure of full-thickness perforation following endoscopic submucosal dissection of a gastric tumor near an anastomosis, using the reopenable clip-over-line method
Authors: Tatsuma Nomura, Shinya Sugimoto, Hirohisa Hisada, Jun Oyamada, Keiichi Ito, Akira Kamei
Journal: Endoscopy (2023)

Early gastric tumors can be completely resected using endoscopic submucosal dissection (ESD). However, ESD is challenging for tumors located above a gastric anastomosis, and intraoperative perforation can create difficulty [1]. We have developed a closure technique using reopenable clips with a hole in one jaw (or "arm") of the clip (Sureclip 8 mm; Micro-Tech, China) and a line (nylon, 0.22 mm) that allows complete closure of thick mucosa and muscle layers, such as those in the stomach. We have previously described the reopenable clip-over-line (RCOL) technique [2] [3]. In this report, we present complete defect closure using the RCOL method after perforation during ESD at a gastric anastomosis.
OTHR-01. SUCCESSFUL DEVELOPMENT OF A LOCAL-REGIONAL POST-MORTEM BRAIN TUMOR DONATION PROGRAM
Authors: Melissa Mark, Kelsey Sowell, Deborah Zapata
Journal: Neuro-Oncology (2023)

Abstract Patient tumor tissue is vital to development of therapeutic interventions in the setting of refractory CNS tumors. Patients and families who participate in tumor donation (TD) report meaning making and improved bereavement outcomes. Provider discomfort is a significant barrier to autopsy participation. Families who are not approached for tumor donation report distress or a feeling of a missed opportunity. Our center developed a process to offer all patients who died from their disease the option to participate in TD as a standard of care. Discussions around TD are best done in the context of a multidisciplinary team well known to the patient and family lead by the treating oncologist. Opportunities to discuss TD present themselves at predictable time points in the disease trajectory: day one talk, treatment discussion, time of recurrence, clinical deterioration, advance care planning discussions, end of life, and immediately-post mortem. Our practice is in the setting of a free-standing children’s hospital. We are not a phase one site. In 2022 seven patients in our neuro-oncology program died from progressive disease. Seven of seven chose to participate in TD. We partnered with a regional phase one center and SWIFTY foundation to coordinate logistics and enrollment. All tumor procurements occurred off site at the funeral home selected by each family. To facilitate family comfort with TD a local team member was present at the time of harvest and kept family updated in process in real time via phone call at the following time points: time of harvest, completion of harvest, tissue arrival at research site. Future directions include offering structured post-mortem visits with families to review research findings with primary treating oncologist in conjunction with the research team and conducting prospective studies with bereaved families to better understand the impact of TD on bereavement.
A light in the dark: Peroral cholangioscopy provides a new strategy for difficult cannulation in pancreaticobiliary maljunction
Authors: Wen-Lin Zhang, Ning Zhong, Rui Ji
Journal: Endoscopy (2023)

A 56-year-old man suffered from epigastric pain for 5 days with elevated amylase (2600 IU/L), and computed tomography indicated acute pancreatitis. Magnetic resonance cholangiopancreatography showed the confluence between dilated biliary and pancreatic ducts ([Fig. 1]), and endoscopic ultrasound indicated a 1.7-cm common channel, suggesting a pancreaticobiliary maljunction (PBM). Subsequent endoscopic retrograde cholangiopancreatography (ERCP) showed pancreatic duct opacification when conducting cholangiography ([Fig. 2]). Considering the symptoms of acute pancreatitis and high amylase, we attempted stent implantation to conduct pancreatic juice drainage and relieve the abdominal pain.
OTHR-12. LOCATION-RELEVANT GROWTH FACTOR DEPENDENCE ON THE FORMATION OF PEDIATRIC BRAIN TUMOR ORGANOIDS FROM PDOX MODELS AND PATIENT SAMPLES
Authors: Milagros Suarez, Sophie Xiao, Aalaa Abdallah, Michael DuCuypere, Sandi Lam, Nitin Wadhwani, Yuchen Du, Xiao-Nan Li
Journal: Neuro-Oncology (2023)

Abstract Brain cancer constitutes the most common type of childhood malignancies and the leading cause of death in children. Despite recent advances in diagnostic methods, surgical techniques as well as chemo- and radio-therapeutic strategies; the survival rates in many types of malignant pediatric brain tumors remain dismal, with &amp;lt;25% of children with high grade glioma surviving five years after initial diagnosis and nearly all patients with diffuse intrinsic pontine glioma succumbing to the disease within 9-12 months. Moreover, even among brain tumor survivors, many patients are left with long-term cognitive and/or neuroendocrine sequalae. Therefore, more efficacious therapeutic modalities that can improve the patient’s quality of life and increase their survival are urgently needed. 3D organoid cultures have arisen as clinically relevant and molecularly accurate in vitro brain tumor model systems for preclinical drug testing. These models have demonstrated to faithfully recapitulate the genomic and phenotypic complexities of the original tumor and thereby, can reliably predict the patient response to treatment. Recognizing the impact of the tumor microenvironment and the brain developmental stage on brain tumor growth, we developed a novel protocol to evaluate the impact of tumor location-related niche factors on the development of brain tumoral organoids. Utilizing different growth factor combinations that are unique/selective to different regions of brain development, we were able to develop 39 PDOX-derived organoids from a total of 40 PDOX models tested (success rate: 97.5%) and 23 patient-derived organoids from a total of 29 patient samples tested (success rate: 79%). Furthermore, cellular characterization studies revealed the replication of an heterogenous cell population. Altogether, our study identifies differences on growth factor dependence for the formation of organoids from brain tumors of different locations and demonstrates that PDOX models are valuable tools for the development and optimization of protocols for organoid model establishment.
EPEN-07. A MULTICENTER STUDY OF POOR PROGNOSIS CHROMOSOME 1Q GAIN AND/OR 6Q LOSS IN POSTERIOR FOSSA A EPENDYMOMA SHOWS INCREASED PREVALENCE FROM 20% AT DIAGNOSIS TO 60% AT FIRST RECURRENCE
Authors: Andrew Donson, Kelsey Bertrand, Kent Riemondy, Dexiang Gao, Bridget Sanford, Gregory Norris, Rui Fu, Nicholas Willard, Andrea Griesinger, Vladimir Amani, Enrique Grimaldo, Todd Hankinson, Ffyona Booker, Richard Grundy, Kristian Pajtler, David Ellison, Timothy Ritzmann
Journal: Neuro-Oncology (2023)

Abstract Ependymoma (EPN) posterior fossa group A (PFA) has the highest rate of recurrence and the worst prognosis of all EPN types. At relapse, it is typically incurable even with re-resection and re-irradiation. The biology of recurrent PFA EPN remains largely unknown, which hinders clinical advances. In this longitudinal large multicenter study, we examined matched samples of primary and recurrent disease from PFA EPN patients (n=95) to investigate the biology of recurrence. DNA methylomic data was used to measure copy number variants (CNVs), revealing progressive large scale chromosome gains and losses in successive recurrences. These CNV changes were dominated by chromosome 1q gain and/or 6q loss (1q+/6q-), both previously identified as high-risk factors in PFA EPN, which were present in ~20% at presentation but increased to ~60% at 1st recurrence. Because 6q testing is not routinely performed, this very high incidence at recurrence has not been previously reported. Evolution of chromosomal aberrations was further explored using CNV analysis of single-nuclei RNAseq on approximately 46,000 PFA EPN cells from 6 matched pairs of primary and 1st relapse tumors that harbored CNV changes at recurrence. No evidence of rare subclones in primary tumors was observed, suggesting that chromosomal rearrangement events occur after initial presentation. Cellular and molecular characteristics associated with CNVs were examined by single-nuclei RNAseq, bulk transcriptomic analysis and immunohistochemistry, revealing that 1q+/6q- PFA have a significantly higher mitotic index, increased proportions of proliferative epithelial progenitors and decreased differentiated neoplastic subpopulations. Multivariate survival analyses showed that cases with 1q gain or 6q loss at 1st recurrence were significantly more likely to recur than cases with no 1q or 6q change. The high prevalence of 1q+/6q- at recurrence and the associated shortened survival, suggest that both these abnormalities should be routinely tested for, and used for trial stratification.
MDB-13. CURRENT STATUS OF DIAGNOSIS AND TREATMENT FOR HIGH-RISK STAGE M2/M3 NON-WNT SUBTYPES MEDULLOBLASTOMA IN SOUTH CHINA
Authors: Linbo Cai, Mingyao Lai, Juan Li
Journal: Neuro-Oncology (2023)

Abstract OBJECTIVE To analyze the current diagnosis and treatment status of high-risk stage M2/M3 non-WNT types medulloblastoma in China, and explore the optimal treatment option. METHODS The inclusion criteria were as follows: (1) age≤18 years old; (2) medulloblastoma was diagnosed by surgical pathology at initial diagnosis; (3) molecular subtyping: non-WNT types; (4) Chang’s stage: M2/M3. Exclusion criteria: cases of WNT molecular subtype were excluded. Clinical data of the patients were included in the analysis, and the overall survival rate and the survival difference between each molecular subtype group were analyzed. RESULTS A total of 247 children with medulloblastoma under 18 years old were admitted to Guangdong Sanjiu Brain Hospital from January 1, 2017, to December 31, 2022. In line with the inclusion criteria, a total of 31 children were enrolled in the present study. All patients were treated with conventional radiotherapy and chemotherapy according to the Chinese Guidelines for diagnosing and treating medulloblastoma. The median age of enrolled patients was 5 years (range 1-15 years), counting 21 males and 10 females. According to the Chang staging system, 16 patients were in the M2 stage, and 15 were in the M3 stage. 8, 11, and 12 patients were in Group 3, Group 4, and SHH molecular subgroups, respectively. Survival analysis showed that the 5-year survival rate of 31 children was 50.2%, and there was no significant difference in the 5-year survival rate between different molecular subgroups (p=0.57). CONCLUSIONS The overall prognosis of high-risk M2 and M3 staged medulloblastoma is poor. Except for the WNT subtype, the optimal treatment strategy for medulloblastoma with metastasis is still worth exploring.
LGG-04. CLINICALLY RELEVANT MODELING OF FUSION-DRIVEN PEDIATRIC LOW GRADE GLIOMAS USING DROSOPHILA MELANOGASTER
Authors: Geena Jung, Payal Jain, Zizhuo Liang, Feng Li, Komal Rathi, Xin Chen, Joshua Straka, Mateusz Koptyra, Stephanie Sanchez-maldonado, Anahita Fathikazerooni, Ariana Familiar, Ali Nabavizadeh, Angela Waanders, Xi Huang, Adam Resnick, Yuanquan Song
Journal: Neuro-Oncology (2023)

Abstract Pediatric low-grade gliomas (PLGGs) are the most common brain tumors in children, with varying degrees of brain invasion. Recent whole-genome sequencing has identified a rare gene fusion involving RAF1, a RAF isoform. Unlike other RAF fusions, RAF1 fusions are resistant to existing RAF inhibitors. Therefore, aside from surgical resection with adjuvant chemotherapy and radiation therapy, there are few targeted therapeutic alternatives for RAF1-fusion-driven PLGGs. Despite the prevalence and challenges this disease presented, our understanding of PLGGs was limited by a lack of genetic models. We ultimately picked Drosophila melanogaster as our model organism due to the conservation of major signaling pathways between flies and humans. Furthermore, this connection between humans and flies, coupled with other technical advantages associated with this model organism, like short generation cycle and its powerful genetic toolbox, makes Drosophila melanogaster an ideal organism to study the genesis and progression of PLGGs. With the help of the GAL4/UAS system, we established four fusion-driven PLGG fly genetic models and found that glial overexpression of QKI-RAF1, a fusion gene in pilocytic astrocytomas, induces an invasion-like phenotype with aberrant glial migration. This migration defect was suppressed by glial overexpression of repulsive guidance signaling receptors Robo2 or PlexA/B, indicating the dysregulation of repulsive guidance signaling pathways. Immunostaining coupled with quantitative analysis revealed that Robo2 expression is downregulated in migrating tumor cells in flies, which is recapitulated in mouse astrocytes overexpressing QKI-RAF1 and PLGG patients with RAF fusions. We further broaden our findings by profiling the tumor transcriptomes, revealing potential downstream effectors, including the G protein-coupled receptor GPR180/CG9304, and inhibition of which suppresses tumor invasion in flies. Taken together, we present the PLGG fly model system, leading to the discovery of Robo2, Plexins, and GPR180/CG9304 as potential therapeutic targets.
METB-10. EXPLAINABLE ARTIFICIAL INTELLIGENCE REVEALS DNA METHYLATION PATTERNS UNDERLYING BRAIN TUMOR CLASSIFICATION
Authors: Salvatore Benfatto, Volker Hovestadt
Journal: Neuro-Oncology (2023)

Abstract Over 100 different molecular classes of brain tumors are recognized across histopathological grades and age groups. Their precise diagnosis is crucial for prognostication and appropriate treatment decisions, particularly in pediatric patients. Recently, a random forest-based classifier trained on genome-wide DNA methylation profiles has been developed to guide the accurate classification of these tumors. Over recent years, this classifier has been applied to tens-of-thousands of patient tumors all over the world. Clinical and basic neuro-oncology research would benefit greatly from a detailed understanding of the underlying artificial intelligence decision process. However, why the algorithm arrives at a certain prediction remains unclear. Here, we develop an interpretable framework to explain the model’s decisions and to uncover DNA methylation patterns distinguishing different tumor classes. Using this approach, we demonstrate both global and local differences across epigenetic landscapes. For instance, the model frequently uses DNA methylation probes in CpG islands to distinguish IDH mutant gliomas from other tumor classes. Tumor classes associated with global hypomethylation are distinguished by probes located in broad heterochromatic domains. At the level of individual genes, we find hundreds of promoter and gene body regions specifically methylated or unmethylated in specific classes. In general, we detect a high degree of redundant information in the dataset, with multiple genes across the genome distinguishing individual tumor classes, and many CpG probes representing each gene. These findings explain the technical robustness of the array-based classifier, and provide a starting point for the design of more compact point of care assays. The results of our approach are provided to the research community via an interactive web interface. We hope that this resource will help to build up trust in the machine learning-based classifier in clinical settings, foster biomarker discovery, and enable cancer epigenome research in the context of the central nervous system tumors.